biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	90d*)	7d	90d**)
								downloads		commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	21 months	263	12	86362	7391
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.5	6 months	18	5	45633	4866	0	0
3	simple spreadsheet extractor	Basic spreadsheet content extraction using apache poi (...)	Stuart Owen, Finn Bacall, Quyen Nguyen	0.13.4	6 weeks	5	1	39689	3187	0	3
4	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	9 months	14	11	36437	3537	0	0
5	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.3.2	3 days	17	6	34051	5773	6	12
6	t2 server	Support for interacting with taverna 2 server (...)	Robert Haines, Finn Bacall	1.3.0	3 days	2	...	28098	2103
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.6.2	11 months	13	1	23694	2658	0	0
8	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	3 years	4	...	22838	2187	0	0
9	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	21 months		...	22828	3410	0	0
10	biomart	A Ruby api for interacting with biomart services (...)	Darren Oakley	0.2.3	3 years	17	4	22250	1568	0	0
11	taverna t2flow	Support for interacting with taverna 2 workflows (...)	Finn Bacall, Robert Haines, David Withers et al.	0.5.1	11 months			21601	1564
12	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.9	11 weeks	55	28	19695	2283	8	200
13	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	2 years	6	2	17950	1544	0	0
14	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.4.1	13 months	9	5	17770	4129	0	0
15	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	2 years	10	31	17019	2127
16	search biomodel	Interfaces with biomodel search engine (...)	Niall Beard	2.1.6	2 years	1	...	15231	1222	0	0
17	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	2 years	5	...	14731	1860	0	0
18	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	2 years	4	2	14280	1481	0	0
19	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...)	Pjotr Prins	2.0.2	3 months	12	...	13604	2230	0	0
20	obo parser	A simple obo file handler (...)	mjy	0.3.7	3 years	4	...	13331	982	0	0
21	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	2 years	9	...	10641	1079	0	0
22	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.8	9 months	7	5	10458	1186
23	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	1.0.0	9 months	8	20	10263	1398	0	0
24	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	7 weeks	11	2	9724	2464	0	10
25	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	2 years	1	...	9000	954	0	0
26	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	3 years	2	1	8958	768	0	0
27	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	17 months	14	3	8850	1697	0	0
28	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.6	9 months	8	1	8568	934	0	0
29	nexus parser	A nexus file format (phylogenetic inference) parser in (...)	mjy	1.1.4	3 years	1	...	8529	533	0	0
30	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	18 months	5	...	8093	560	0	0
31	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.1	6 months	1	...	8014	957	0	0
32	taverna baclava	Ruby support for the baclava file format (...)	Robert Haines	1.0.1	12 months	1	...	7956	476
33	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	4 years	4	...	7834	617	0	0
34	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor (...)	mjy	0.2.6	3 years	1	...	7688	509	0	0
35	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	2 years	2	...	7527	776	0	0
36	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	20 months	8	...	7377	712	0	0
37	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	2 years	7	2	7342	635	0	0
38	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	21 months	5	...	7230	920	0	0
39	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	5 years			7207	688
40	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	2 years	2	...	7193	781	0	0
41	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	3 years	3	...	7153	642	0	0
42	bioportal	Supports linking of models within a ror application (...)	Stuart Owen, Quyen Nguyen	2.2	11 months		...	7124	597	0	0
43	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	7 years	22	1	6687	482	0	0
44	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	3 years	4	...	6572	555	0	0
45	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	2 years	29	14	6277	498	0	0
46	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	3 years	1	...	5971	460	0	0
47	bio polyploid tools	Tool to work with polyploids, ngs and molecular (...)	Ricardo H. Ramirez-Gonzalez	0.6.0	2 weeks	2	1	5887	2582	0	13
48	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	2 years	2	...	5575	715	0	0
49	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	3 years	4	...	5285	471	0	0
50	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	4 years	9	...	5223	418
51	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	19 months	11	2	5086	1027	0	0
52	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	3 years	1	...	5082	477	0	0
53	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	2 years	2	...	4883	479	0	0
54	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	22 months	2	1	4817	621
55	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	4 years	38	5	4768	247	0	0
56	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	17 months	3	...	4554	622	0	0
57	taverna player	Taverna player is a rails plugin to run (...)	Robert Haines	0.11.0	2 days	4	3	4361	1001
58	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	2 years			4066	471
59	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	2 years	1	1	4011	484	0	0
60	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	4 years	1	...	4001	311	0	0
61	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	2 years	2	...	3984	471
62	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	2 years	2	...	3978	459	0	0
63	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	3 years	1	...	3967	313	0	0
64	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	2 years	4	1	3730	338	0	0
65	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	3 years	2	1	3699	350
66	bio velvet	Parser to work with file formats used in (...)	Ben J Woodcroft	0.6.0	7 weeks		...	3658	1388	0	8
67	bio vcf	Fast multi-threaded vcf parser (...)	Pjotr Prins	0.8.2	9 weeks	15	7	3544	1431	0	83
68	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	3 years	1	...	3444	307	0	0
69	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	17 months			3336	634
70	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	2 years	1	...	3273	318	0	0
71	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	3 years	1	...	3228	320	0	0
72	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	2 years			3202	461
73	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	21 months		...	3086	472	0	0
74	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	18 months	1	...	3074	471	0	0
75	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	2 years	1	...	2893	323	0	0
76	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	2 years	1	...	2826	312	0	0
77	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	2 years	2	...	2731	313	0	0
78	bio polymarker db batch	Server for polymarker. to be used with cron (...)	Ricardo H. Ramirez-Gonzalez	0.4.0	4 months		...	2564	1156	0	0
79	publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.6	8 months	3	16	2449	383
80	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)	Andrei Rozanski	1.3.0	11 months	1	...	2179	621	0	0
81	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	4 years	4	...	2071	144	0	0
82	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	4 years	3	...	2066	165	0	0
83	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	3 years		1	2062	166	0	0
84	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	5 years	1	...	1987	153	0	0
85	rubyBHL	Rubybhl is a simple request/response wrapper for the (...)	Matt Yoder	0.2.1	12 months	6	...	1918	180	0	0
86	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	3 years	1	...	1803	154	0	0
87	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	3 years	1	...	1792	149	0	0
88	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	3 years		...	1769	158	0	0
89	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	3 years	2	...	1768	169	0	0
90	bio velvet underground	Bindings to some internals of the velvet assembler (...)	Ben Woodcroft	0.3.0	7 weeks		1	1763	992	0	9
91	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	3 years	3	...	1748	161	0	0
92	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	18 months	1	...	1746	310	0	0
93	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	3 years	1	...	1735	160	0	0
94	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	3 years	4	...	1719	155	0	0
95	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	2 years	3	...	1697	159	0	0
96	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1684	166
97	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	17 months	3	1	1665	311	0	0
98	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1655	148	0	0
99	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	3 years	1	...	1652	157	0	0
100	taxonifi	A general purpose framework for scripted handling of (...) development/stable	mjy	0.2.0	23 months	2	...	1628	169	0	0
101	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	17 months			1610	308
102	bio biostars analytics	Biostars data-mining and statistical analysis (...)	Joachim Baran	0.2.0	10 months			1594	476
103	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	2 years	1	1	1563	172	0	0
104	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	2 years			1464	168
105	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1449	157	0	0
106	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	3 years	1	...	1433	104	0	0
107	ref2bibtex	Pass a full citation, get the bibtex back, (...)	Matt Yoder	0.0.3	3 months		...	1408	737	0	0
108	bio commandeer	Dead simple method of running shell commands from (...)	Ben J. Woodcroft	0.1.0	13 months		...	1357	313	0	0
109	bio express beta diversity	Interface for express beta diversity (...)	Ben J. Woodcroft	0.1.0	13 months		...	1343	321
110	bio repeatmasker	Bio-repeatmasker (...)	Andrei Rozanski	0.0.3	13 months			1319	310
111	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	2 years		...	1204	159	0	0
112	bio cigar	A parser for cigar format alignments (...)	Ben J Woodcroft	0.1.0	12 months	4	...	1183	322	0	0
113	nbio cloudquery	Client for xoopit's cloudquery api (...)	Cameron Walters, nb.io	0.1.5	5 years	5	...	1181	377
114	bio samtools server	Web server for bio-samtools (...)	homonecloco	0.1.2	9 months		...	1040	324	0	0
115	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	20 months	2	...	994	166	0	0
116	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	19 months		...	931	160	0	0
117	bio locus	Fast storage and comparison of chr+pos(+alt) locations (...)	Pjotr Prins	0.0.6	4 months			836	334
118	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a (...)	Cameron Walters, Randy Reddig	1.0.3	6 years	90	1	603	205	0	0
119	bio exominer	Mine publications for gene names (...)	Pjotr Prins	0.0.3	12 months		...	602	165	0	0
120	genomichdt	A restful service for sharing genomic data (...)	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	11 months			540	189
121	bio sra	A sequence read archive (sra) download script and (...)	Ben J. Woodcroft	0.2.0	10 weeks	1	...	505	505	0	11
122	bio kseq	Ruby inferface for kseq.h by heng li for (...)	Fedor Gusev	0.0.2	7 months		...	449	171	0	1
123	bark	A Ruby wrapper on the open tree api (...) beta	Matt Yoder	0.0.2	5 months		...	396	198	0	0
124	bio qtlHD	(...) pre		pre				395	25
125	bio rocker	Rocker (...) new	Luis (Coto) Orellana, Luis M. Rodriguez-R	0.1.01	5 weeks			379	379
126	bio faidx	Tools to work with fasta files, indexed with (...)	homonecloco	0.0.1	4 months		...	363	184	0	0
127	bio blat tools	Tools to manipulate blat files from the command (...)	homonecloco	0.1.0	4 months		...	356	172	0	0
128	nbio css http request	Csshttprequest is cross-domain ajax using css (...)	Cameron Walters, Randy Reddig	0.1	6 years			309	100
129	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives (...)	Naohisa Goto	0.0.0	3 months		...	303	184	0	0
130	bio location rdfize	Faldo location output method for bio::location in BioRuby (...)	Joachim Baran, Naohisa Goto	0.0.0	3 months		...	296	177	0	0
131	bio mummer	Helper methods for reading .delta files (...) new	robsyme	0.1.0	2 weeks		...	144	144	0	11
132	bio primer3	(...) pre		pre				140	33

*) gem downloads (total & last 90 days) from rubygems.org as of 2015-03-01
**) number of commits on GitHub (last 7 days & last 90 days)